Full QC for 14568_STD_Nidhi-Arianna_Plasma_Pan-cancer_TMT16plex_NS_MP_Eduardo_20230327_18.57
Completed on 2023-03-28 14:32:39
Software
Pipeline DOI: 10.5281/zenodo.3548311 (resolves to latest version)
| Software | Version |
|---|---|
| lehtiolab/ddamsproteomics | v2.11 |
| Nextflow | v22.10.5 |
| MSGF+ | v2020.03.14 |
| Dinosaur | v1.2.0 |
| Kronik | v2.20 |
| Luciphor2 | v2020_04_03 |
| Percolator | v3.04.0 |
| msstitch | v3.11 |
| OpenMS | v2.5.0-HEAD-HASH-NOTFOUND-HEAD-HASH-NOTFOUND |
| DEqMS | v1.6.0 |
Warnings
No warnings
Protein/peptide level QC
Summary
| Experiment set | Proteins ID and quant. (1%FDR) | Proteins ID and quant. (gene centric, 1%FDR) | Peptides (unique, 1%FDR) | Peptides/protein (unique, median) | Peptides/protein (genecentric, unique, median) | PSMs (total) | PSMs/protein for quant (median) | PSMs/protein for quant (genecentric, median) |
|---|---|---|---|---|---|---|---|---|
| Set1 | 5733 | 5701 | 32320 | 3 | 3 | 132509 | 4 | 3 |
| Set2 | 1471 | 1549 | 13850 | 3 | 3 | 116313 | 5 | 4 |
| Set3 | 1872 | 1921 | 16487 | 3 | 3 | 118568 | 5 | 4 |
Overlap
Peptides
| IDed in # overlapping sets | |
|---|---|
| 1 | 23208 |
| 2 | 4600 |
| 3 | 10083 |
Proteins
| Proteins ID (1%FDR) | IDed in # overlapping sets |
|---|---|
| 4284 | 1 |
| 424 | 2 |
| 1315 | 3 |
Gene names
| Proteins ID (gene centric, 1%FDR) | IDed in # overlapping sets |
|---|---|
| 4296 | 1 |
| 491 | 2 |
| 1299 | 3 |
ENSGs
| IDed in # overlapping sets | |
|---|---|
| 1 | 4106 |
| 2 | 467 |
| 3 | 1184 |
PTMs
Summary
PTM site count
Median centered isobaric normalization factors
Peptides
| Experiment set | Isob. channel | Norm. factor |
|---|---|---|
| Set1 | tmt16plex_126 | -0.06086110917296761 |
| Set1 | tmt16plex_127N | 0.11068622402670059 |
| Set1 | tmt16plex_127C | -0.02486996838843325 |
| Set1 | tmt16plex_128N | -0.02300261843959106 |
| Set1 | tmt16plex_128C | 0.051993806032074374 |
| Set1 | tmt16plex_129N | -0.09386451090497694 |
| Set1 | tmt16plex_129C | -0.03983887252272211 |
| Set1 | tmt16plex_130N | -0.0628405658855451 |
| Set1 | tmt16plex_130C | 0.049064966096107554 |
| Set1 | tmt16plex_131N | -0.008130763169126531 |
| Set1 | tmt16plex_131C | -0.049417308157240214 |
| Set1 | tmt16plex_132N | -0.15934906282864247 |
| Set1 | tmt16plex_132C | 0.0 |
| Set1 | tmt16plex_133N | 0.028840418530721834 |
| Set1 | tmt16plex_133C | -0.04173666425389655 |
| Set1 | tmt16plex_134N | -0.21407867451855367 |
| Set2 | tmt16plex_126 | -0.3211329736357893 |
| Set2 | tmt16plex_127N | 0.16546092822544844 |
| Set2 | tmt16plex_127C | -0.3534008217425413 |
| Set2 | tmt16plex_128N | -0.25184983851384857 |
| Set2 | tmt16plex_128C | 0.13322427895321098 |
| Set2 | tmt16plex_129N | -0.18181874162971035 |
| Set2 | tmt16plex_129C | 0.14169756398416533 |
| Set2 | tmt16plex_130N | 0.028203888586133985 |
| Set2 | tmt16plex_130C | -0.7898407451922864 |
| Set2 | tmt16plex_131N | 0.23637700480522295 |
| Set2 | tmt16plex_131C | 0.0 |
| Set2 | tmt16plex_132N | 0.03866017522670617 |
| Set2 | tmt16plex_132C | -0.13142426882530955 |
| Set2 | tmt16plex_133N | 0.1522611859231473 |
| Set2 | tmt16plex_133C | -0.08207070421716622 |
| Set2 | tmt16plex_134N | 0.23841903282900034 |
| Set3 | tmt16plex_126 | -0.32089295516491845 |
| Set3 | tmt16plex_127N | -0.23020358171973232 |
| Set3 | tmt16plex_127C | -0.002137024372352414 |
| Set3 | tmt16plex_128N | 0.21908863092821207 |
| Set3 | tmt16plex_128C | 0.4333034857229898 |
| Set3 | tmt16plex_129N | -0.11176174268310302 |
| Set3 | tmt16plex_129C | -0.06601071142346093 |
| Set3 | tmt16plex_130N | 0.19080910455854472 |
| Set3 | tmt16plex_130C | 0.24503025661991362 |
| Set3 | tmt16plex_131N | -0.133240412866229 |
| Set3 | tmt16plex_131C | 0.3162146478439567 |
| Set3 | tmt16plex_132N | 0.23088511461111239 |
| Set3 | tmt16plex_132C | 0.09402128587886249 |
| Set3 | tmt16plex_133N | 0.15439671969207325 |
| Set3 | tmt16plex_133C | 0.029918112990890755 |
| Set3 | tmt16plex_134N | 0.0 |
Proteins
| Experiment set | Isob. channel | Norm. factor |
|---|---|---|
| Set1 | tmt16plex_126 | -0.0035401536311354675 |
| Set1 | tmt16plex_127N | 0.09931422285240643 |
| Set1 | tmt16plex_127C | -0.018227138801556464 |
| Set1 | tmt16plex_128N | 0.08233497752071628 |
| Set1 | tmt16plex_128C | 0.0629948023923923 |
| Set1 | tmt16plex_129N | -0.03937719477776014 |
| Set1 | tmt16plex_129C | 0.025350091215356585 |
| Set1 | tmt16plex_130N | 0.03584003712234729 |
| Set1 | tmt16plex_130C | 0.030014548953740672 |
| Set1 | tmt16plex_131N | -0.013596490990669619 |
| Set1 | tmt16plex_131C | -0.06363795297568231 |
| Set1 | tmt16plex_132N | -0.17226474905452704 |
| Set1 | tmt16plex_132C | 0.0 |
| Set1 | tmt16plex_133N | 0.023091892033666017 |
| Set1 | tmt16plex_133C | -0.050323616757339096 |
| Set1 | tmt16plex_134N | -0.22441327198422245 |
| Set2 | tmt16plex_126 | -0.2822219483695818 |
| Set2 | tmt16plex_127N | 0.15524319881512572 |
| Set2 | tmt16plex_127C | -0.39831501586605356 |
| Set2 | tmt16plex_128N | -0.2873310591366418 |
| Set2 | tmt16plex_128C | 0.09024013031497358 |
| Set2 | tmt16plex_129N | -0.1827524773101743 |
| Set2 | tmt16plex_129C | 0.05491846407429879 |
| Set2 | tmt16plex_130N | 0.05669727488355747 |
| Set2 | tmt16plex_130C | -0.7912779838872499 |
| Set2 | tmt16plex_131N | 0.10832798469240146 |
| Set2 | tmt16plex_131C | 0.0 |
| Set2 | tmt16plex_132N | 0.0013382673842521342 |
| Set2 | tmt16plex_132C | -0.13874300866765488 |
| Set2 | tmt16plex_133N | 0.06352140749877044 |
| Set2 | tmt16plex_133C | -0.12313516411635561 |
| Set2 | tmt16plex_134N | 0.11408414397617328 |
| Set3 | tmt16plex_126 | -0.40546086769885115 |
| Set3 | tmt16plex_127N | -0.31564241127227 |
| Set3 | tmt16plex_127C | -0.07125206698409059 |
| Set3 | tmt16plex_128N | 0.09993592241179527 |
| Set3 | tmt16plex_128C | 0.4598148699100566 |
| Set3 | tmt16plex_129N | -0.1659314465336088 |
| Set3 | tmt16plex_129C | -0.07420644102558605 |
| Set3 | tmt16plex_130N | 0.17547132784868058 |
| Set3 | tmt16plex_130C | 0.08906676527034207 |
| Set3 | tmt16plex_131N | -0.1117417749844618 |
| Set3 | tmt16plex_131C | 0.1840978210956985 |
| Set3 | tmt16plex_132N | 0.16662649134470353 |
| Set3 | tmt16plex_132C | 0.03708678524267839 |
| Set3 | tmt16plex_133N | 0.1701029426210745 |
| Set3 | tmt16plex_133C | 0.07009435965353639 |
| Set3 | tmt16plex_134N | 0.0 |
Gene names
| Experiment set | Isob. channel | Norm. factor |
|---|---|---|
| Set1 | tmt16plex_126 | -0.002731124041632782 |
| Set1 | tmt16plex_127N | 0.09919047843961648 |
| Set1 | tmt16plex_127C | -0.016422312709927667 |
| Set1 | tmt16plex_128N | 0.08209306806665495 |
| Set1 | tmt16plex_128C | 0.06305339158036549 |
| Set1 | tmt16plex_129N | -0.04015423823335418 |
| Set1 | tmt16plex_129C | 0.02535939789328623 |
| Set1 | tmt16plex_130N | 0.037095872974676425 |
| Set1 | tmt16plex_130C | 0.029654637182545684 |
| Set1 | tmt16plex_131N | -0.012890082725119711 |
| Set1 | tmt16plex_131C | -0.06287446063258528 |
| Set1 | tmt16plex_132N | -0.17204749871758285 |
| Set1 | tmt16plex_132C | 0.0 |
| Set1 | tmt16plex_133N | 0.02438459775816737 |
| Set1 | tmt16plex_133C | -0.04926394156034064 |
| Set1 | tmt16plex_134N | -0.22300724041123487 |
| Set2 | tmt16plex_126 | -0.28114896387263233 |
| Set2 | tmt16plex_127N | 0.15771558351159243 |
| Set2 | tmt16plex_127C | -0.40025909258196357 |
| Set2 | tmt16plex_128N | -0.28430843825308116 |
| Set2 | tmt16plex_128C | 0.08612524084707474 |
| Set2 | tmt16plex_129N | -0.17206613854169817 |
| Set2 | tmt16plex_129C | 0.05289451797501776 |
| Set2 | tmt16plex_130N | 0.056884833526407164 |
| Set2 | tmt16plex_130C | -0.7979119214343751 |
| Set2 | tmt16plex_131N | 0.1087747074679708 |
| Set2 | tmt16plex_131C | 0.0 |
| Set2 | tmt16plex_132N | -0.0021823519653842993 |
| Set2 | tmt16plex_132C | -0.14179872892638912 |
| Set2 | tmt16plex_133N | 0.06774053907820132 |
| Set2 | tmt16plex_133C | -0.11807356428317561 |
| Set2 | tmt16plex_134N | 0.11209522257849969 |
| Set3 | tmt16plex_126 | -0.40135222107239965 |
| Set3 | tmt16plex_127N | -0.31303040853791764 |
| Set3 | tmt16plex_127C | -0.06435691886114014 |
| Set3 | tmt16plex_128N | 0.1093655402450775 |
| Set3 | tmt16plex_128C | 0.46303219056908773 |
| Set3 | tmt16plex_129N | -0.1667732021920214 |
| Set3 | tmt16plex_129C | -0.0737773196727094 |
| Set3 | tmt16plex_130N | 0.176668274783216 |
| Set3 | tmt16plex_130C | 0.08930865392695075 |
| Set3 | tmt16plex_131N | -0.1050000771453341 |
| Set3 | tmt16plex_131C | 0.1846565934831368 |
| Set3 | tmt16plex_132N | 0.16724100593116464 |
| Set3 | tmt16plex_132C | 0.04257811633491748 |
| Set3 | tmt16plex_133N | 0.17663638697015926 |
| Set3 | tmt16plex_133C | 0.0772691409264814 |
| Set3 | tmt16plex_134N | 0.0 |
ENSGs
| Experiment set | Isob. channel | Norm. factor |
|---|---|---|
| Set1 | tmt16plex_126 | -0.004400699449474299 |
| Set1 | tmt16plex_127N | 0.09932979768127126 |
| Set1 | tmt16plex_127C | -0.015633906493410787 |
| Set1 | tmt16plex_128N | 0.08115514617969577 |
| Set1 | tmt16plex_128C | 0.06504867933239611 |
| Set1 | tmt16plex_129N | -0.04148981775079985 |
| Set1 | tmt16plex_129C | 0.023125895349230152 |
| Set1 | tmt16plex_130N | 0.03549973080571611 |
| Set1 | tmt16plex_130C | 0.030394955409101865 |
| Set1 | tmt16plex_131N | -0.011730512923685765 |
| Set1 | tmt16plex_131C | -0.06384573204702004 |
| Set1 | tmt16plex_132N | -0.17221176921115777 |
| Set1 | tmt16plex_132C | 0.0 |
| Set1 | tmt16plex_133N | 0.023434838180903306 |
| Set1 | tmt16plex_133C | -0.04916089331046791 |
| Set1 | tmt16plex_134N | -0.2230735457082602 |
| Set2 | tmt16plex_126 | -0.29397624167102343 |
| Set2 | tmt16plex_127N | 0.15231059694076254 |
| Set2 | tmt16plex_127C | -0.4094412751364622 |
| Set2 | tmt16plex_128N | -0.2843889019706545 |
| Set2 | tmt16plex_128C | 0.07724258674553575 |
| Set2 | tmt16plex_129N | -0.16362039211850465 |
| Set2 | tmt16plex_129C | 0.04631986754546347 |
| Set2 | tmt16plex_130N | 0.05409065551472203 |
| Set2 | tmt16plex_130C | -0.8129045085526041 |
| Set2 | tmt16plex_131N | 0.11543863095661244 |
| Set2 | tmt16plex_131C | 0.0 |
| Set2 | tmt16plex_132N | -0.014493024122090858 |
| Set2 | tmt16plex_132C | -0.16182067264067346 |
| Set2 | tmt16plex_133N | 0.07014273705065044 |
| Set2 | tmt16plex_133C | -0.12481953902296894 |
| Set2 | tmt16plex_134N | 0.10387834581068667 |
| Set3 | tmt16plex_126 | -0.3941063584955984 |
| Set3 | tmt16plex_127N | -0.3081277164344538 |
| Set3 | tmt16plex_127C | -0.054331702815025196 |
| Set3 | tmt16plex_128N | 0.12288565037373189 |
| Set3 | tmt16plex_128C | 0.4632743673687898 |
| Set3 | tmt16plex_129N | -0.16986047687796102 |
| Set3 | tmt16plex_129C | -0.07162532036410241 |
| Set3 | tmt16plex_130N | 0.18004583994448264 |
| Set3 | tmt16plex_130C | 0.09858150453208747 |
| Set3 | tmt16plex_131N | -0.1050000771453341 |
| Set3 | tmt16plex_131C | 0.19960285549365953 |
| Set3 | tmt16plex_132N | 0.1643994359582095 |
| Set3 | tmt16plex_132C | 0.056508653197749226 |
| Set3 | tmt16plex_133N | 0.18295462898346315 |
| Set3 | tmt16plex_133C | 0.09553249551893472 |
| Set3 | tmt16plex_134N | 0.0 |
Identifications
Peptides
Proteins
Gene names
ENSGs
Precursor area intensity
Peptides
Proteins
Gene names
ENSGs
Isobaric intensities
Peptides
Proteins
Gene names
ENSGs
